Slow algae, fast fungi: Exceptionally high nucleotide substitution rate differences between lichenized fungi Omphalina and their symbiotic green algae Coccomyxa

Molecular Phylogenetics and Evolution

Volumn 29, Issue 3, 2003, Pages 629-640

  Zoller, Stefan ^a,b   Lutzoni, François ^a  

^a DUKE UNIVERSITY   (United States)

^b North Carolina Supercomputing Center   (United States)

Author keywords

Basidiomycota; Coccomyxa; Coevolution; Inhabitant exhabitant; Lichens; Mutualistic symbiosis; Nucleotide substitution rates; Omphalina

Indexed keywords

ALGAE; BASIDIOMYCOTA; CHLOROPHYTA; COCCOMYXA; FUNGI; OMPHALINA;

EID: 0344287478     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1055-7903(03)00215-X     Document Type: Article

References (46)

1. Ahmadjian, V., 1970. The lichen symbiosis: its origin and evolution. In: Dobzhansky, T., Hecht, M.K., Steere, W.C. (Eds.), Evolutionary Biology, vol. 4. Appleton-Century-Crofts, New York, pp. 163-184.
2. Armaleo, D., Clerc, P., 1995. A rapid and inexpensive method for the purification of DNA from lichens and their symbionts. Lichenologist 27 (3), 207-213.
3. Ashen, J.B., Goff, L.J., 2000. Molecular and ecological evidence for species specificity and coevolution in a group of marine algal-bacterial symbioses. Appl. Environ. Microbiol. 66 (7), 3024-3030.
4. Axelrod, R., Hamilton, W.D., 1981. The evolution of cooperation. Science 211, 1390-1396.
5. Bischoff, H.W., Bold, H.C., 1963. Phycological studies. IV. Some soil algae from Enchanted Rock and related algal species. University of Texas Publication No. 6318, pp. 1-95.
6. Clark, M.A., Moran, N.A., Baumann, P., Weregreen, J.J., 2000. Cospeciation between bacterial endosymbionts (Buchnera) and a recent radiation of aphids (Uroleucon) and pitfalls of testing for phylogenetic congruence. Evolution 54 (2), 517-525.
7. Doebeli, M., Knowlton, N., 1998. The evolution of interspecific mutualisms. Proc. Natl. Acad. Sci. USA 95, 8676-8680.
8. Felsenstein, J., 1978. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27, 401-410.
9. Felsenstein, J., 1981. A likelihood approach to character weighting and what it tells us about parsimony and compatibility. Biol. J. Linn. Soc. 16, 183-196.
10. Friedl, T., Büdel, B., 1996. Photobionts. In: Nash, T.H. (Ed.), Lichen Biology. Cambridge University Press, Cambridge, pp. 8-23.
11. Gast, R.J., Caron, D.A., 1996. Molecular phylogeny of symbiotic dinoflagellates from planktionic foraminifera and radiolaria. Mol. Biol. Evol. 13 (9), 1192-1197.
12. Hawksworth, D.L., 1988. The fungal partner. In: Galun, M. (Ed.), Handbook of Lichenology, vol. 1. CRC Press, Boca Raton, FL, pp. 35-38.
13. Hawksworth, D.L., 1991. The fungal dimension of biodiversity: magnitude, significance, and conservation. Mycol. Res. 95, 641-655.
14. Hawksworth, D.L., Kirk, P.M., Sutton, B.C., Pegler, D.N., 1995. Dictionary of Fungi. Cambridge University Press, Cambridge.
15. Herre, E.A., Knowlton, N., Mueller, U.A., Rehner, S.A., 1999. The evolution of mutualism: exploring the paths between conflict and cooperation. Trends Ecol. Evol. 14 (2), 49-53.
16. Huelsenbeck, J.P., Rannala, B., Yang, Z., 1997. Statistical tests of host-parasite cospeciation. Evolution 51, 410-419.
17. Johnson, K.P., Cruickshank, R.H., Adams, R.J., Smith, V.C., Page, R.D.M., Clayton, D.H., 2003. Dramatically elevated rate of mitochondrial substitution in lice (Insecta: Phthiraptera). Mol. Phyl. Evol. 26, 231-242.
18. Kishino, H., Hasegawa, M., 1989. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. J. Mol. Evol. 29, 170-179.
19. Kishino, H., Miyata, T., Hasegawa, M., 1990. Maximum likelihood inference of protein phylogeny and the origin of chloroplasts. J. Mol. Evol. 30, 151-160.
20. Kranner, I., Lutzoni, F., 1999. Evolutionary consequences of transition to a lichen symbiotic state and physiological adaptation to oxidative damage associated with poikilohydry. In: Lerner, H.R. (Ed.), Plant Response to Environmental Stresses: From Phytohormones to Genome Reorganization. Marcel Dekker, New York, pp. 591-628.
21. Kroken, S., Taylor, J.W., 2000. Phylogenetic species, reproductive mode, and specificity of the green alga Trebouxia froming lichens with the fungal genus Letharia. Bryologist 103 (4), 645-660.
22. Lanave, C., Preparata, G., Saccone, C., Serio, G., 1984. A new method for calculating evolutionary substitution rates. J. Mol. Evol. 20, 86-93.
23. Law, R., Lewis, D.H., 1983. Biotic environments and the maintenance of sex - some evidence from mutualistic symbioses. Biol. J. Linn. Soc. 20, 249-276.
24. Lutzoni, F., 1997. Phylogeny of lichen-and non-lichen-forming omphalinoid mushrooms and the utility of testing for combinability among multiple data sets. Syst. Biol. 46 (3), 373-406.
25. Lutzoni, F., Pagel, M., 1997. Accelerated evolution as a consequence of transitions to mutualism. Proc. Natl. Acad. Sci. USA 94, 11422-11427.
26. Lutzoni, F., Vilgalys, R., 1995. Omphalina (Basidiomycota, Agaricales) as a model system for the study of coevolution in lichens. Cryptogamic Bot. 5, 71-81.
27. Lutzoni, F., Pagel, M., Reeb, V., 2001. Major fungal lineages are derived from lichen symbiotic ancestors. Nature 411, 937-940.
28. Mathews, D.H., Sabina, J., Zuker, M., Turner, D.H., 1999. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288, 911-940.
29. Moncalvo, J.M., Lutzoni, F., Rehner, S.A., Johnson, J., Vilgalys, R., 2000. Phylogenetic relationships of agaric fungi based on nuclear large subunit ribosomal DNA sequences. Syst. Biol. 49, 278-305.
30. Moran, N.A., Wernegreen, J.J., 2000. Lifestyle evolution in symbiotic bacteria: insights from genomics. Trends Ecol. Evol. 15 (8), 321-326.
31. Moran, N.A., Dohlen, C.D., Baumann, P., 1995. Faster evolutionary rates in endosymbiotic bacteria than in cospeciating insect hosts. J. Mol. Evol. 41, 727-731.
32. Page, R., 1995. TreeMap 1.0b, Software and Users Guide. Distributed by the author (http://taxonomy.zoology.gla.ac.uk/rod/tree-map.html), University of Glasgow, UK.
33. Paulsrud, P., Lindblad, P., 1998. Sequence variation of the tRNA(Leu)intron as a marker for genetic diversity and specificity of symbiotic cyanobacteria in some lichens. Appl. Environ. Microbiol. 64, 310-315.
34. Piercey-Normore, M.D., DePriest, P.T., 2001. Algal switching among lichen symbioses. Am. J. Bot. 88 (8), 1490-1498.
35. Posada, D., Crandall, K.A., 1998. Modeltest: testing the model of DNA substitution. Bioinformatics 14 (9), 817-818.
36. Rambaut, A., Grassly, N.C., 1997. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13, 235-238.
37. Redhead, S.A., Lutzoni, F., Moncalvo, J.-M., Vilgalys, R., 2002. Phylogeny of agarics: partial systematics solutions for core omphalinoid genera in the Agaricales (euagarics). Mycotaxon 83, 19-57.
38. Shimodaira, H., Hasegawa, M., 1999. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 16, 1114-1116.
39. Swofford, D.L., 2000. PAUP*. Phylogenetic Analysis Using Parsimony *(and Other Methods), Version 4. Sinauer Associates, Sunderland, MA.
40. Tamura, K., Nei, M., 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10 (3), 512-526.
41. Trivers, R.L., 1971. The evolution of reciprocal altruism. Quart. Rev. Biol. 46, 35-57.
42. Tschermak-Woess, E., 1988. The algal partner. In: Galun, M. (Ed.), Handbook of Lichenology, vol. 1. CRC Press, Boca Raton, FL, pp. 39-92.
43. Vilgalys, R., Hester, M., 1990. Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species. J. Bacteriol. 172 (8), 4238-4246.
44. Wheeler, W.C., 1990. Combinatorial weights in phylogenetic analysis: a statistical parsimony procedure. Cladistics 6, 269-275.
45. White, T.J., Bruns, T., Lee, S., Taylor, J.W., 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis, M.A., Gelfan, D.H., Sninsky, J.J., White, T. (Eds.), PCR Protocols. Academic Press, New York, pp. 315-322.
46. Zuker, M., Mathews, D.H., Turner, D.H., 1999. Algorithms and thermodynamics for RNA secondary structure prediction: a practical guide. In: Barciszewski, J., Clark, B.F.C. (Eds.), RNA Biochemistry and Biotechnology. NATO ASI Series. Kluwer Academic Publishers, Dordrecht, pp. 11-43.